NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE164779 Query DataSets for GSE164779
Status Public on Nov 30, 2021
Title Hierarchical chromatin regulation during blood formation uncovered by single-cell sortChIC
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary Post-translational histone modifications modulate chromatin packing to regulate gene expression. How chromatin states, both at euchromatic and at heterochromatic regions, underlie cell fate decisions in single cells is relatively unexplored. We develop sort assisted single-cell chromatin immunocleavage (sortChIC) and apply it to map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in hematopoietic stem and progenitor cells (HSPCs), and mature blood cells in the mouse bone marrow. During differentiation, HSPCs acquire distinct active chromatin states that depend on the specific cell fate, mediated by cell type-specifying transcription factors. By contrast, most regions that gain or lose repressive marks during differentiation do so independent of the specific cell fate. Joint profiling of active H3K4me1 and repressive H3K9me3 in single cells demonstrates that cell types within the myeloid lineage have distinct active chromatin regulation but share a similar myeloid-specific heterochromatin-repressed state. Our results suggest a hierarchical chromatin regulation program during hematopoiesis, by which heterochromatin dynamics define differentiation trajectories and lineages, while euchromatin dynamics establish cell types within lineages.
 
Overall design single-cell sortChIC data on K562 and mouse bone marrow cells
 
Contributor(s) Zeller P, Yeung J, Viñas Gaza H, de Barbanson B, Bhardwaj V, Florescu M, van Oudenaarden A
Citation(s) 36539617
Submission date Jan 13, 2021
Last update date May 31, 2023
Contact name Jake Yeung
E-mail(s) jakeyeung@gmail.com
Organization name Hubrecht Institute
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584T
Country Netherlands
 
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (106)
GSM5018601 BM-H3K27me3-BM_Round2Only-CelltypesMerged.BM-H3K27me3-BM_Round2Only-CelltypesMerged
GSM5018602 K562-H3K27me3-37Uor75Umerged-K562_Ncells.K562-H3K27me3-37Uor75Umerged-K562_Ncells
GSM5018603 BM-H3K4me3-BM_Round1Round2Merged-CelltypesMerged.BM-H3K4me3-BM_Round1Round2Merged-CelltypesMerged
Relations
BioProject PRJNA691938
SRA SRP301626

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE164779_RAW.tar 119.4 Gb (http)(custom) TAR (of BAM, CSV, TXT)
GSE164779_countmat_K562_k27me3.txt.gz 12.5 Mb (ftp)(http) TXT
GSE164779_countmat_K562_k4me1.txt.gz 14.8 Mb (ftp)(http) TXT
GSE164779_countmat_K562_k4me3.txt.gz 4.5 Mb (ftp)(http) TXT
GSE164779_countmat_K562_k9me3.txt.gz 9.9 Mb (ftp)(http) TXT
GSE164779_countmat_bonemarrow_allmerged_k27me3.txt.gz 15.2 Mb (ftp)(http) TXT
GSE164779_countmat_bonemarrow_allmerged_k4me1.txt.gz 33.8 Mb (ftp)(http) TXT
GSE164779_countmat_bonemarrow_allmerged_k4me3.txt.gz 4.3 Mb (ftp)(http) TXT
GSE164779_countmat_bonemarrow_allmerged_k9me3.txt.gz 8.2 Mb (ftp)(http) TXT
GSE164779_metadata_K562_k27me3.txt.gz 39.5 Kb (ftp)(http) TXT
GSE164779_metadata_K562_k4me1.txt.gz 39.8 Kb (ftp)(http) TXT
GSE164779_metadata_K562_k4me3.txt.gz 33.3 Kb (ftp)(http) TXT
GSE164779_metadata_K562_k9me3.txt.gz 37.7 Kb (ftp)(http) TXT
GSE164779_metadata_bonemarrow_LSKstained_k27me3.txt.gz 591.6 Kb (ftp)(http) TXT
GSE164779_metadata_bonemarrow_LSKstained_k4me1.txt.gz 711.7 Kb (ftp)(http) TXT
GSE164779_metadata_bonemarrow_LSKstained_k4me3.txt.gz 754.2 Kb (ftp)(http) TXT
GSE164779_metadata_bonemarrow_LSKstained_k9me3.txt.gz 930.4 Kb (ftp)(http) TXT
GSE164779_metadata_bonemarrow_allmerged_k27me3.txt.gz 179.2 Kb (ftp)(http) TXT
GSE164779_metadata_bonemarrow_allmerged_k4me1.txt.gz 405.1 Kb (ftp)(http) TXT
GSE164779_metadata_bonemarrow_allmerged_k4me3.txt.gz 258.3 Kb (ftp)(http) TXT
GSE164779_metadata_bonemarrow_allmerged_k9me3.txt.gz 805.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.